C. Henry

发表

High-throughput generation, optimization and analysis of genome-scale metabolic models

Rick L. Stevens, C. Henry, M. DeJongh, 2010, Nature Biotechnology.

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Adam M. Feist, B. Palsson, P. Karp, 2007, Molecular systems biology.

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data

Ronald C. Taylor, José P. Faria, R. Overbeek, 2016, Front. Microbiol..

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Rida Assaf, Fangfang Xia, Robert Olson, 2016, Nucleic Acids Res..

Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3‐hydroxypropanoate

V. Hatzimanikatis, C. Henry, L. Broadbelt, 2010, Biotechnology and bioengineering.

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

Kevin P. Keegan, Peter E. Larsen, J. Gilbert, 2011, Microbial Informatics and Experimentation.

Thermodynamics-based metabolic flux analysis.

V. Hatzimanikatis, C. Henry, L. Broadbelt, 2007, Biophysical journal.

Group contribution method for thermodynamic analysis of complex metabolic networks.

Matthew D. Jankowski, V. Hatzimanikatis, C. Henry, 2008, Biophysical journal.

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

Andrew D. Hanson, Christopher S. Henry, Samuel M. D. Seaver, 2018, The Plant journal : for cell and molecular biology.

The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair.

C. Henry, A. Hanson, P. Abraham, 2021, Biochemistry.

Automated genome annotation and metabolic model reconstruction in the SEED and Model SEED.

R. Overbeek, C. Henry, M. DeJongh, 2013, Methods in molecular biology.

Enzymes as Parts in Need of Replacement - and How to Extend Their Working Life.

A. Millar, C. Henry, A. Hanson, 2020, Trends in plant science.

The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes

James G. Jeffryes, Michael B. Mundy, José P. Faria, 2020, bioRxiv.

Genome-scale thermodynamic analysis of Escherichia coli metabolism.

Matthew D. Jankowski, V. Hatzimanikatis, C. Henry, 2006, Biophysical journal.

Genome-wide metabolic network reconstruction of the picoalga Ostreococcus.

Elias W. Krumholz, C. Henry, I. Libourel, 2012, Journal of experimental botany.

Connecting genotype to phenotype in the era of high-throughput sequencing.

Rick L. Stevens, Kevin P. Keegan, R. Overbeek, 2011, Biochimica et biophysica acta.

KBase: The United States Department of Energy Systems Biology Knowledgebase

Rick L. Stevens, James J. Davis, Kevin P. Keegan, 2018, Nature Biotechnology.

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

Thomas D. Niehaus, V. de Crécy-Lagard, C. Henry, 2016, BMC Genomics.

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Rick L. Stevens, Thomas D. Niehaus, R. Overbeek, 2014, Proceedings of the National Academy of Sciences.

Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.

C. Henry, A. Joachimiak, M. Endres, 2016, The Biochemical journal.

Microbial Community Metabolic Modeling: A Community Data‐Driven Network Reconstruction

Hans C. Bernstein, Ronald C. Taylor, C. Henry, 2016, Journal of cellular physiology.

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

E. Ruppin, C. Henry, S. Seaver, 2015, Front. Plant Sci..

Computational discovery of biochemical routes to specialty chemicals

Linda J. Broadbelt, Christopher S. Henry, Vassily Hatzimanikatis, 2004 .

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Rick L Stevens, Rick L. Stevens, Christopher S Henry, 2009, Genome Biology.

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

Fangfang Xia, Rick L. Stevens, Christopher S. Henry, 2012, Nucleic acids research.

Constructing and Analyzing Metabolic Flux Models of Microbial Communities

José P. Faria, T. Khazaei, C. Henry, 2016 .

A genomic catalog of Earth’s microbiomes

Vincent J. Denef, Natalia N. Ivanova, Paramvir S. Dehal, 2020, Nature Biotechnology.

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities

Ronan M. T. Fleming, Janaka N. Edirisinghe, R. Fleming, 2020, bioRxiv.

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Fangfang Xia, Eytan Ruppin, Daniel J. Dwyer, 2016, PLoS Comput. Biol..

Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium

Janaka N. Edirisinghe, C. Henry, N. Gupta, 2019, Microbiology Resource Announcements.

Reconstruction and Analysis of Central Metabolism in Microbes.

José P. Faria, Benjamin H. Allen, C. Henry, 2018, Methods in molecular biology.

Metabolite Damage and Metabolite Damage Control in Plants.

O. Fiehn, V. de Crécy-Lagard, C. Henry, 2016, Annual review of plant biology.

Knowledgebase and Computing for Systems Biology 220 KBase : An Integrated Knowledgebase for Predictive Biology and Environmental Research

Rick L. Stevens, Paramvir S. Dehal, B. Davison, 2012 .

TranSyT, an innovative framework for identifying transport systems

José P. Faria, C. Henry, Filipe Liu, 2021, bioRxiv.

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

Fangfang Xia, Miguel Rocha, Isabel Rocha, 2014, Briefings Bioinform..

Modeling central metabolism and energy biosynthesis across microbial life

Fangfang Xia, Rick L. Stevens, Christopher S. Henry, 2016, BMC Genomics.

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

Fangfang Xia, Rick L. Stevens, Robert A. Edwards, 2012, PloS one.

Publisher Correction: A genomic catalog of Earth’s microbiomes

Natalia N. Ivanova, Paramvir S. Dehal, José P. Faria, 2020, Nature biotechnology.

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

C. Henry, R. Dias, Pedro Escudeiro, 2022, Current research in microbial sciences.

A roadmap for the functional annotation of protein families: a community perspective

Benjamin M. Gyori, Lucy J. Colwell, Ian K. Blaby, 2022, Database J. Biol. Databases Curation.

Metabolic Reconstruction and Modeling Microbial Electrosynthesis

Janaka N. Edirisinghe, Jack A Gilbert, Christopher S Henry, 2016, bioRxiv.

Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium

José P. Faria, Janaka N. Edirisinghe, J. Gilbert, 2019, Microbiology Resource Announcements.

Exploring the diversity of complex metabolic networks

Chunhui Li, Linda J. Broadbelt, Christopher S. Henry, 2005, Bioinform..

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction.

José P. Faria, C. Henry, Fangfang Xia, 2014, Methods in molecular biology.

Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of Liberibacter

Michael J. Davis, C. Henry, E. Triplett, 2014, PloS one.

A novel signal transduction protein: Combination of solute binding and tandem PAS‐like sensor domains in one polypeptide chain

C. Henry, A. Joachimiak, M. Endres, 2017, Protein science : a publication of the Protein Society.

Reconstruction of regulatory network models and reconciliation with gene expression data

Vincent Fromion, Miguel Rocha, Isabel Rocha, 2015 .

Plant B vitamin pathways and their compartmentation: a guide for the perplexed.

Svetlana Gerdes, Andrew D Hanson, Christopher S Henry, 2012, Journal of experimental botany.

Genome-scale modeling of the primary-specialized metabolism interface.

C. Henry, S. Seaver, Kathleen Beilsmith, 2022, Current opinion in plant biology.

Evolution of substrate specificity in a retained enzyme driven by gene loss

Janaka N. Edirisinghe, C. Henry, A. Joachimiak, 2017, eLife.

A directed-overflow and damage-control N-glycosidase in riboflavin biosynthesis.

Bing Wang, James G. Jeffryes, James G Jeffryes, 2015, The Biochemical journal.

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

Thomas D. Niehaus, V. de Crécy-Lagard, C. Henry, 2016, BMC Genomics.

Metabolite Damage and Damage Control in a Minimal Genome

Lijie Sun, K. Wise, J. Glass, 2021, bioRxiv.

Competitive and cooperative metabolic interactions in bacterial communities.

Roded Sharan, Eytan Ruppin, Shiri Freilich, 2011, Nature communications.

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum.

Paramvir S. Dehal, A. Arkin, C. Henry, 2021, Current Plant Biology.

'Nothing of chemistry disappears in biology': the Top 30 damage-prone endogenous metabolites.

Oliver Fiehn, James G. Jeffryes, Thomas D. Niehaus, 2016, Biochemical Society transactions.

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

Oliver Fiehn, James G. Jeffryes, Ricardo L. Colastani, 2015, Journal of Cheminformatics.

Draft Genome Sequence of a Multidrug-Resistant Klebsiella quasipneumoniae subsp. similipneumoniae Isolate from a Clinical Source

Keith E. J. Tyo, C. Henry, W. W. Lathem, 2016, Genome Announcements.

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Matthew DeJongh, Nicholas Chia, James G. Jeffryes, 2020, Nucleic Acids Res..

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Ronan M. T. Fleming, Janaka N. Edirisinghe, R. Fleming, 2023, Nature Biotechnology.

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

José P. Faria, C. Henry, S. H. Chan, 2022, bioRxiv.

Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome.

José P. Faria, Benjamin H. Allen, C. Henry, 2021, Methods in molecular biology.

ORT: A workflow linking genome-scale metabolic models with reactive transport codes

D. Hoyt, C. Henry, R. Versteeg, 2021, bioRxiv.

TranSyT, the Transport Systems Tracker

José P. Faria, C. Henry, Filipe Liu, 2021 .

Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions

C. Henry, L. McCue, Dennis G. Thomas, 2021, ACS omega.

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Matthew DeJongh, Nicholas Chia, James G. Jeffryes, 2020, Nucleic Acids Res..

Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium

José P. Faria, J. Gilbert, C. Henry, 2020, Microbiology Resource Announcements.

Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987

José P. Faria, Janaka N. Edirisinghe, J. Gilbert, 2020, Microbiology Resource Announcements.

MEMOTE for standardized genome-scale metabolic model testing

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2020, Nature Biotechnology.

Methods for automated genome-scale metabolic model reconstruction.

Miguel Rocha, Isabel Rocha, José P. Faria, 2018, Biochemical Society transactions.

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

Miguel Rocha, Isabel Rocha, Matthew DeJongh, 2016, Front. Microbiol..

Modeling central metabolism and energy biosynthesis across microbial life

Rick L. Stevens, R. Overbeek, C. Henry, 2016, BMC Genomics.

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

Nathan D. Price, Christopher S. Henry, Nicholas Chia, 2014, PLoS Comput. Biol..

Author Correction: A genomic catalog of Earth’s microbiomes

Natalia N. Ivanova, Paramvir S. Dehal, José P. Faria, 2021, Nature biotechnology.

The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering

Jenelle A. Patterson, A. Millar, C. Henry, 2021, Proceedings of the National Academy of Sciences.

Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB)

Andrew D. Hanson, Christopher S. Henry, Katherine J. Harrison, 2016, Front. Microbiol..

Frontiers in metabolic reconstruction and modeling of plant genomes.

Andrew D Hanson, Christopher S Henry, Samuel M D Seaver, 2012, Journal of experimental botany.

Long-term phenotypic evolution of bacteria

Christopher S. Henry, Dennis Vitkup, D. Vitkup, 2014, Nature.

Building the blueprint of life

Rick L. Stevens, Ross Overbeek, R. Overbeek, 2010, Biotechnology journal.

Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1

Keith E J Tyo, Christopher S Henry, C. Henry, 2017, The Journal of infectious diseases.

Metabolite damage and repair in metabolic engineering design.

James G. Jeffryes, James G Jeffryes, Andrew D Hanson, 2017, Metabolic engineering.

Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Steffen Klamt, Anne Richelle, Hyun Uk Kim, 2018, bioRxiv.

MEMOTE for standardized genome-scale metabolic model testing

Ronan M. T. Fleming, Adam M. Feist, Zachary A. King, 2020, Nature Biotechnology.

A pathway for every product? Tools to discover and design plant metabolism.

James G. Jeffryes, José P. Faria, James G Jeffryes, 2018, Plant science : an international journal of experimental plant biology.

Respiratory energy demands and scope for demand expansion and destruction

C. Henry, J. Amthor, Ulschan Bathe, 2022, Plant physiology.

Elucidating genomic gaps using phenotypic profiles

Forest Rohwer, Veronika Vonstein, Christopher S. Henry, 2014 .

A plastidial pantoate transporter with a potential role in pantothenate synthesis.

V. de Crécy-Lagard, C. Henry, A. Fernie, 2018, The Biochemical journal.

Enabling comparative modeling of closely related genomes: example genus Brucella

James J. Davis, José P. Faria, R. Overbeek, 2014, 3 Biotech.

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Adam M. Feist, P. Karp, M. Krummenacker, 2007, Molecular systems biology.

Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Eytan Ruppin, Shiri Freilich, Christopher S. Henry, 2014, PloS one.

Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models

Miguel Rocha, Rick L. Stevens, Christopher S. Henry, 2010, IWPACBB.

Metabolic Network Modeling for Computer‐Aided Design of Microbial Interactions

Doraiswami Ramkrishna, Christopher S. Henry, Hans C. Bernstein, 2018 .

A functional microbiome catalog crowdsourced from North American rivers

Annika C. Mosier, José P. Faria, Janaka N. Edirisinghe, 2023, bioRxiv.

High-throughput generation and optimization of genome-scale metabolic models

Matthew DeJongh, Rick L. Stevens, Aaron A. Best, 2009 .

Information- and Communication-Centric Approach in Cell Metabolism for Analyzing Behavior of Microbial Communities

C. Henry, M. Pierobon, A. Freiburger, 2023, bioRxiv.

Machine Learning-Driven Phenotype Predictions based on Genome Annotations

Janaka N. Edirisinghe, C. Henry, Qizh Zhang, 2023, bioRxiv.